Research Computing & Harvard-Smithsonian Center for Astrophysics, Harvard University

Nov 7-8, 2014

9:00 am - 4:30 pm

Instructors:
Daniel Chen, Ivan Gonzalez

Helpers:
Christopher Erdmann, Bob Freeman, Jean Roth, Peter Williams

General Information

Software Carpentry's mission
is to help scientists and engineers become more productive
by teaching them basic lab skills for computing
like program design, version control, data management, and task automation.
This two-day hands-on workshop will cover basic concepts and tools;
participants will be encouraged to help one another
and to apply what they have learned to their own research problems.

Who:
The course is aimed at undergraduate and graduate students and other researchers.

Managing Scientific Projects

Organizing your files and directories

Building pipelines with make

Working remotely in a cluster

Setup

To participate in a Software Carpentry workshop,
you will need working copies of the software described below.
Please make sure to install everything
(or at least to download the installers)
before the start of your workshop.

Overview

Editor

When you're writing code, it's nice to have a text
editor that is optimized for writing code, with features
like automatic color-coding of key words.
The default text editor on Mac OS X and Linux is usually set to Vim,
which is not famous for being intuitive.
if you accidentally find yourself stuck in it,
try typing the escape key,
followed by ':q!' (colon, lower-case 'q', exclamation mark),
then hitting Return
to return to the shell.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you
more power to do more tasks more quickly with your
computer.

Git

Git is a state-of-the-art version control system. It
lets you track who made changes to what when and has
options for easily updating a shared or public version of
your code on github.com.

Python

Python is becoming very popular in scientific computing,
and it's a great language for teaching general programming concepts due to its easy-to-read syntax.
We teach with Python version 2.7,
since it is still the most widely used.
Installing all the scientific packages for Python individually can be a bit difficult,
so we recommend an all-in-one installer.

Software Carpentry Installer

If the file opens directly in the browser select File→Save Page As
to download it to your computer.

Double click on the file to run it.

Editor

nano is the editor installed by the Software Carpentry Installer,
it is a basic editor integrated into the lesson material.

Notepad++ is a
popular free code editor for Windows.
Be aware that you must add its installation directory to your system path
in order to launch it from the command line
(or have other tools like Git launch it for you).
Please ask your instructor to help you do this.

Mac OS X

Bash

The default shell in all versions of Mac OS X is bash,
so no need to install anything. You access bash from
the Terminal (found
in /Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.

Editor

Git

For OS X 10.8 and higher, install Git for Mac by downloading and running
the installer.
For older versions of OS X (10.5-10.7) use the most recent available
installer for your OS available
here. Use the Leopard installer for 10.5 and the Snow Leopard
installer for 10.6-10.7.

Python

Use all of the defaults for installation
except
make sure to check Make Anaconda the default Python.

Linux

Bash

The default shell is usually bash,
but if your machine is set up differently
you can run it by opening a terminal and typing bash.
There is no need to install anything.

Git

If Git is not already available on your machine you can try
to install it via your distro's package manager
(e.g. apt-get or yum).

Editor

Kate is one option for Linux users.
In a pinch, you can use nano,
which should be pre-installed.

Python

We recommend the all-in-one scientific Python installer
Anaconda.
(Installation requires using the shell and if you aren't
comfortable doing the installation yourself just
download the installer and we'll help you at the boot
camp.)

Download the installer that matches your operating
system and save it in your home folder.

Open a terminal window.

Type

bash Anaconda-

and then press
tab. The name of the file you just downloaded should
appear.

Press enter. You will follow the text-only
prompts. When there is a colon at the bottom of the
screen press the down arrow to move down through the
text. Type yes and press enter to approve
the license. Press enter to approve the default
location for the files. Type yes and
press enter to prepend Anaconda to
your PATH (this makes the Anaconda
distribution the default Python).

All operating systems

Get a Research Computing cluster account

You will need an account at the Reseearch Computing Odyssey cluster
during the workshop.
To get an account: